Re: [vmtk-users] convert into c++

[Lia S. <lia...@po...>]

Em 18-03-2012 15:25, Luca Antiga escreveu:
> Excellent, I'm happy to know you're on the right track.
> Have fun!
>
> Luca
>
>
> On Mar 18, 2012, at 1:30 PM, Lia Silva wrote:
>
>> Em 18-03-2012 11:56, Luca Antiga escreveu:
>>> Hi Lia,
>>>  that's not quite what I intended. I'll you a few more explicit 
>>> suggestions:
>>>
>>> 1) all the algorithms in vmtk are already in C++. The fact that 
>>> you're using them
>>> in vmtk scripts is just for convenience. Note that this does not 
>>> impose *any* overhead,
>>> speed-wise.
>>>
>>> 2) make sure you understand why you need to have a C++-only code. Is
>>> it for speed only? See point 1). Is if because you want to 
>>> incorporate vmtk in
>>> a purely C++ program? This would make more sense.
>>>
>>> 3) every algorithm in vmtk is a VTK class. If you know how to 
>>> program in C++ using VTK,
>>> you know how to program in C++ using vmtk. So, make sure you are 
>>> proficient writing
>>> VTK code before you move on with vmtk. There's a great resource of 
>>> examples here:
>>> http://www.vtk.org/Wiki/VTK/Examples/Cxx
>>>
>>> 4) Once you have addressed 1-3, have a look into vmtk/vmtkScripts 
>>> and identify the scripts
>>> you're interested in and take a look at what classes are used. For 
>>> instance, the code for
>>> vmtksurfacetriangle is
>>>
>>>         cleaner = vtk.vtkCleanPolyData()
>>>         cleaner.SetInput(self.Surface)
>>>         cleaner.Update()
>>>
>>>         triangleFilter = vtk.vtkTriangleFilter()
>>>         triangleFilter.SetInput(cleaner.GetOutput())
>>>         triangleFilter.Update()
>>>
>>>         self.Surface = triangleFilter.GetOutput()
>>>
>>> which in C++ would become
>>>
>>>         vtkCleanPolyData* cleaner = vtkCleanPolyData::New();
>>>         cleaner->SetInput(surface);
>>>         cleaner->Update();
>>>
>>>         vtkTriangleFilter* triangleFilter = vtkTriangleFilter::New();
>>>         triangleFilter->SetInput(cleaner->GetOutput());
>>>         triangleFilter->Update();
>>>
>>>         surface = triangleFilter->GetOutput();
>>>
>>> As you see, the high-level code is almost exactly the same, and in both
>>> cases, the call to Update triggers code that is already written in C++.
>>>
>>> Hope this helps clarifying, but most of all, what you should clarify 
>>> is point 2, i.e. what
>>> is the need you're trying to address when you say you want pure C++ 
>>> code.
>>>
>>> Best regards
>>>
>>> Luca
>>>
>>>
>>> On Mar 17, 2012, at 6:41 PM, Lia Silva wrote:
>>>
>>>> Em 17-03-2012 07:40, Luca Antiga escreveu:
>>>>> Dear Lia,
>>>>>  vmtk code presents itself as Python code, but it is in fact a 
>>>>> tiny wrapper
>>>>> on top of C++ code. All algorithms are already implemented in C++ (see
>>>>> vmtk/vtkVmtk directory). If you look for code optimizations, you 
>>>>> should look
>>>>> into the C++ code in that directory.
>>>>> Best regards
>>>>>
>>>>> Luca
>>>>>
>>>>>
>>>>> --
>>>>> Luca Antiga, PhD
>>>>> Cofounder and Principal Scientist, Orobix Srl
>>>>> via L.A. Muratori 3, 24123 Bergamo, Italy
>>>>>
>>>>> orobix: www.orobix.com <http://www.orobix.com/>
>>>>> home: lantiga.github.com <http://lantiga.github.com/>
>>>>> twitter: twitter.com/lantiga <http://twitter.com/lantiga>
>>>>>
>>>>> On Mar 17, 2012, at 12:50 AM, Lia Silva wrote:
>>>>>
>>>>>>
>>>>>>
>>>>>> Hello all!
>>>>>>
>>>>>> How can i convert a vmtk code into c++ code, so i can run it 
>>>>>> faster? The
>>>>>> code in vmtk it's attached.
>>>>>>
>>>>>> Thank you in advance
>>>>>>
>>>>>>
>>>>>>
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>>>>>
>>>> So, it means that i have to implement all in c++ since the 
>>>> beginning? For example, i used the /vmtkimagereader/, so in c++ 
>>>> i've to use/Dicomseriereadprinttagswrite/? And for the 
>>>> /vmtkimagevoiselector /i have to use the 
>>>> /RegionofInterestImageFilter/? Is that it? I'm so confused... Isn't 
>>>> there another way easier and faster? I thought i could convert 
>>>> directly into c++..
>>>>
>>>> Thank you for all your pacience
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>>>
>> Dear Luca,
>>
>> Thank you for the answer. It was very helpfull. In fact, the main 
>> reason i want to use just C++ isn't just to make it faster. This is 
>> also a reason, but i dont know how exactly vmtk works, and i need to 
>> do a automatic/semi-automatic tool for measure the aorta diameter. I 
>> found vmtk by accident and i liked it very much cause its easier to 
>> work with, but i dont know if i can make a automatic tool using it (i 
>> dont know how to automatize the process) . In my circle, nobody knows 
>> vmtk, and my thesis' supervisor just work with c++, so i'm going 
>> forward using vmtk (cause i dont have much experience with c++ and 
>> vmtk scripts are easier for me) and later, i pretend to convert into 
>> c++ so my supervisor can correct it.
>>
>> You gave me an excellent help and now i'm doing the step 4 by seeing 
>> the vmtk scripts. If i have any addicional doubt, i hope i can count 
>> on you.
>>
>> Thank you very much for your pacience and dedication.
>>
>> Best regards
>>
>> Lia
>
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> Versão: 2012.0.1913 / Base de dados de Vírus: 2114/4878 - Data de 
> Lançamento: 03/18/12
>
Dear Luca,

I decided not to convert into C++, for now. It's not worth it.

Now i'm facing two problems: is there a way to automatize some 
parameters? I would like to know if i can change the python code, so i 
dont need to input the parameters manually at the console. In the 
/vmtkimagevoiselector/  i can specify  the coordinates of my cube, and 
if i could insert them in the code it became easier. Same thing with the 
/vmtklevelsetsegmentation/. The parameters are always the same, so can i 
insert them into the code? And how do i do that?

The other issue is: I want to measure the diameter of the ascending 
aorta in nine specifics points. I computed the centerline that gave me 
the central points and the radius in all points since the source till 
the target! But i just need nine points. Is there a way to do that?

For this project i'm doing a lot of steps.. If i could avoid the most of 
them, it would be easier to automatize the process and to decrease the 
processing time. I mean, for compute the centerline its really necessary 
to run the /vmtkimagevoiselector, vmtklevelsetsegmentation/ and 
/vmtkmarchingcubes/?

I'm sorry for the amount of questions, but i'm new at vmtk and programming..

Best regards,

Lia Silva